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73 variant records found |
[show instead phene records] |
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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
| OMIA Variant ID | OMIA Phene-Species ID(s) | Species Name | Breed(s) | Variant Phenotype | Gene | Allele | Variant Type | Variant Effect | Source of Genetic Variant | Pathogenicity Classification* | Reference Sequence | Chr. | g. or m. | c. or n. | p. | Verbal Description | EVA ID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1379 | OMIA:002238-9823 | pig | Bama Xiang Zhu, China (Pig) | Ichthyosis | ABCA12 | splicing | Chemical mutagenesis (ENU) | Not currently ISAG evaluated | Sscrofa11.1 | 15 | g.117250799T>C | Intronic mutation IVS49-727 A>G results in splicing alteration resulting in a 132-nt insertion and a premature stop codon (Wang et al., 2019) | 2019 | 30925591 | ||||||
| 1504 | OMIA:002594-9823 | pig | N-acetyl-galactosamine intestinal concentration | ABO | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 1 | 2.3kb deletion encompassing exon 8 | 2022 | 35477154 | |||||||||
| 1049 | OMIA:002178-9823 | pig | Large White (Pig) | Abortion, BBS9 and BMPER-related | BBS9 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 18 | g.39817373_40029300del | Derks et al. (2018): "a large deletion in complete LD with the SSC18 haplotype of approximately 212kb (position 39,817,373 to 40,029,300), spanning a part of the BBS9 gene ... [and reducing] expression of the downstream BMPER gene" | 2018 | 30231021 | ||||||
| 1281 | OMIA:002306-9823 | pig | German Landrace (Pig) | Infertility and increased litter size | BMP15 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | X | g.44618787C>T | p.(R212*) | "NP_001005155.2:p.R212X" (Flossmann et al., 2021) | 2021 | 33413103 | |||||
| 1254 | OMIA:000576-9823 | pig | Yorkshire (Pig) | Knobbed acrosome defect | BOLL | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 15 | g.101549770_101604750del | 2020 | 32975846 | |||||||
| 1008 | OMIA:001752-9823 | pig | Resistance to PRRS virus | CD163 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 5 | Burkhard et al (2018): "the deletion of exon 7 of CD163 using CRISPR/Cas9 editing" | 2018 | 29925651 | |||||||||
| 177 | OMIA:000636-9823 | pig | Membranoproliferative glomerulonephritis type II | CFH | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 10 | c.3610T>G | p.(I1166R) | CFH is located on Chr10 in Sscrofa10.2 g.2553907T>G, but recorded as 'unplaced/NW_018085100.1' in Sscrofa11.1. | 2002 | 12466119 | The genomic location on Sscrofa11.1 was determined by Stephanie Shields (27/05/2020) | |||||
| 1365 | OMIA:000698-9823 | pig | Myotonia | CLCN1 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 18 | g.6912538_6916702del | 2019 | 31666547 | ||||||||
| 172 | OMIA:001718-9823 | pig | Dwarfism, Schmid metaphyseal chondrodysplasia | COL10A1 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 1 | g.81767089C>T | c.1768G>A | p.(G590R) | 2000 | 11130976 | The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020) | |||||
| 656 | OMIA:000837-9823 | pig | Vitamin D-deficiency rickets, type I | CYP27B1 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 5 | the first of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) | 2003 | 12915218 | |||||||||
| 657 | OMIA:000837-9823 | pig | Vitamin D-deficiency rickets, type I | CYP27B1 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 5 | the second of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) | 2003 | 12915218 | |||||||||
| 784 | OMIA:001986-9823 | pig | Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation | DCLRE1C | splicing | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 10 | g.46845535G>A | 2015 | 26320255 | ||||||||
| 785 | OMIA:001986-9823 | pig | Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation | DCLRE1C | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 10 | g.46851262G>A | p.(Trp267*) | 2015 | 26320255 | |||||||
| 1395 | OMIA:001081-9823 | pig | Duchenne muscular dystrophy | DMD | DMD^ex52del | delins, gross (>20) | Transgenesis via somatic cell nuclear transfer (SCNT) | Not currently ISAG evaluated | X | gene targeting and somatic cell nuclear transfer was used to replace DMD exon 52 with a neomycin resistance cassette | 2013 | 23784375 | ||||||||
| 1457 | OMIA:001888-9823 | pig | Becker muscular dystrophy | DMD | insertion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | X | Aihara et al. (2022): "Analysis of dystrophin mRNA showed a 62 base pair insertion between exons 26 and 27. The insertion was derived from intron 26." | 2022 | 35220848 | ||||||||
| 179 | OMIA:001685-9823 OMIA:001888-9823 | pig | Stress syndrome | DMD | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | X | g.28309227G>A | c.5872C>T | p.(R1958W) | Ensembl VEP was used to identify cDNA position in transcript ENSSSCT00000089893.1, SIFT score 0.01 | rs196952080 | 2012 | 22691118 | ||||
| 1352 | OMIA:002442-9823 | pig | Large White (Pig) | Sperm flagella defect | DNAH17 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 12 | g.3556402_3556414del | Nosková et al. (2021): "intronic 13-bp deletion ... causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17" | 2021 | 33724408 | ||||||
| 1115 | OMIA:002210-9823 | pig | Bama Xiang Zhu, China (Pig) | Congenital hypothyroidosis | DUOX2 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 1 | g.126625620A>G | c.1226A>G | p.(D409G) | ENU mutagenesis was used to create these pigs, the mutation is located within an exonic splicing enhancer motif and causes aberrant splicing of DUOX2 transcripts (Cao et al., 2019) | 2019 | 30651277 | ||||
| 1402 | OMIA:000628-9823 | pig | Marfan syndrome | FBN1 | deletion, small (<=20) | Genome-editing (ZFN) | Not currently ISAG evaluated | Sscrofa11.1 | 1 | g.123246159del | p.(E433Nfs98*) | 2016 | 27074716 | |||||||
| 178 | OMIA:000862-9823 | pig | Resistance to oedema disease (F18 receptor) | FUT1 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.54079560T>C | c.304A>G | p.(T103A) | The variant was initially described as c.307G>A and p.A103T by Vögeli et al. 1997. VEP analysis identified the variant as c.304A>G p.T102A in transcript ENSSSCT00000051297.2 | rs335979375 | 2000 | 11132149 | ||||
| 655 | OMIA:001089-9823 | pig | Blood group system ABO | GGTA1 | O | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 1 | "the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6". | 2011 | 21554350 | ||||||||
| 1195 | OMIA:002268-9823 | pig | Danish Landrace (Pig) | Vitamin C deficiency | GULO | od | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 14 | "This deletion includes 77 bp of exon VIII, 398 bp of intron 7 and 3.7 kbp of intron 8, which leads to a frame shift. The mutant protein is truncated to 356 amino acids, but only the first 236 amino acids are identical to the wild-type GULO protein." (Hasan et al., 2004) | 2004 | 15112110 | |||||||
| 1318 | OMIA:001461-9823 | pig | Wild boar | Gangliosidosis, GM2, type I | HEXA | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 7 | g.60910365C>T | c.1495C>T | p.(R499C) | cDNA positions based on NM_001123221.1 | 2021 | 34119419 | ||||
| 624 | OMIA:001952-9823 | pig | Microtia | HOXA1 | delins, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 18 | g.45478109delinsTC | c.451delinsTC | p.(L151fs) | 2015 | 26035869 | The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: XM_003134844.5 by Stephanie Shields (27/05/2020) | |||||
| 1231 | OMIA:002283-9823 | pig | Large White (Pig) | Arthrogryposis multiplex congenita, KIF21A-related | KIF21A | insertion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 5 | g.70964237_70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT | p.(V41_F42ins*) | (NC_010447.5:g70964237_ g70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT; p.Val41_Phe42insTer) (Fang et al., 2020) | 2020 | 32686171 | |||||
| 391 | OMIA:001216-9823 | pig | Coat colour, roan | KIT | splicing | Naturally occurring variant | Not currently ISAG evaluated | 8 | a U(26) repeat in intron 5 of the KIT gene, which is likely to mediate skipping of exon 5 of the gene in some tissues including skin | 2011 | 21749430 | |||||||||
| 979 | OMIA:000209-9823 | pig | Dominant white | KIT | I | complex rearrangement | Naturally occurring variant | Not currently ISAG evaluated | 8 | This dominant white allele carries at least three causal polymorphisms, namely a 450 kb duplication (originally reported by Johansson Moller (1996); also present in Patch - see OMIA 001743-9825), the splice mutation reported by Marklund et al. (1998) (unique to Dominant white) and smaller duplication(s) (that occur within the 450kb duplication) causing Belt (see OMIA 001745-9825).(with thanks to Leif Andersson). To emphasise the original discovery of the duplication, the ref cited here is Johansson Moller (1996) | 1996 | 8875890 | ||||||||
| 743 | OMIA:001745-9823 | pig | Essex, United Kingdom of Great Britain and Northern Ireland (Pig) Hampshire Down (Sheep) Schwäbisch Hällisches Schwein, Germany (Pig) Wessex Saddleback (Pig) | White belt | KIT | complex rearrangement | Naturally occurring variant | Not currently ISAG evaluated | 8 | Hampshire pigs (belted phenotype) have "a 4.3-kb duplication (DUP2) located ~¼100 kb upstream of KIT and a 23-kb duplication (DUP3) ~100 kb downstream of KIT, which in turn contained a fourth ~4.3-kb duplication (DUP4) not present on wild-type chromosomes". Across four breeds, belted pigs always had DUP2 and DUP4, but some lacked DUP3. | 2012 | 23151514 | ||||||||
| 715 | OMIA:001743-9823 | pig | Coat colour, patch | KIT | duplication | Naturally occurring variant | Not currently ISAG evaluated | 8 | the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle) | 1998 | 9724328 | |||||||||
| 1248 | OMIA:002287-9823 | pig | Bama Xiang Zhu, China (Pig) | Hypopigmentation (piebald) and deafness | KIT | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 8 | g.41485957T>A | c.2418T>A | p.(D806E) | ENU mutagenesis was used to create these pigs, NM_001044525.1; c.2418T>A; NP_001037990.1; p.(D806E) (Xu et al., 2020) | 2020 | 33042408 | ||||
| 1135 | OMIA:001745-9823 | pig | Cinta Senese, Italy (Pig) | White belt | KIT | not known | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 8 | g.41488472C>T | c.2499C>T | p.(P833P) | ENSSSCT00000009679.4:c.2499C>T ENSSSCP00000009430.3:p.Pro833= ENSSSCT00000062378.2:c.*1559C>T Sscrofa10.2 g.43,597,545C>T; Ensembl VEP analysis suggests that this can be a synonymous or 3_prime_UTR_variant depending on the transcript analysed | rs328592739 | 2016 | Reference not in PubMed; see OMIA 001745-9823 for reference details | Ogorevc et al. (2017) reported the EVA ID of this variant as rs328592739 | ||
| 987 | OMIA:000499-9823 | pig | Hypercholesterolaemia | LDLR | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 2 | g.69841413C>T | c.250C>T | p.(R84C) | rs701604154 | 1998 | 9556295 | The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcripts: XM_021080444.1, XM_021080449.1, XM_021080452.1, XM_021080457.1 by Stephanie Shields (27/05/2020) | ||||
| 1401 | OMIA:001213-9823 | pig | Yucatan Miniature, United States of America (Pig) | Hutchinson-Gilford progeria syndrome | LMNA | splicing | Genome-editing (CRISPR-Cas9) | Not currently ISAG evaluated | Sscrofa11.1 | 4 | g.93900345G>A | c.1824C>T | 2019 | 30911407 | ||||||
| 170 | OMIA:001199-9823 | pig | Duroc (Pig) | Red | MC1R | e | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.181461C>T | c.727G>A | p.(A243T) | Variant is called p.(A240T) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2 | rs321432333 | 1998 | 9799269 | ||
| 171 | OMIA:001199-9823 | pig | Duroc (Pig) | Red | MC1R | e | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.181697G>A | c.491C>T | p.(A164V) | Variant is called p.(A161V) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location based in this table are based on transcript ENSSSCT00000022534.2 | rs45435032 | 1998 | 9799269 | ||
| 169 | OMIA:001199-9823 | pig | Hampshire Down (Sheep) | Dominant black | MC1R | E^D2 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.181818C>T | c.370G>A | p.(D124N) | Variant is called p.(D121N) in original paper (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. | rs326921593 | 1998 | 27703696 9799269 | ||
| 168 | OMIA:001199-9823 | pig | Large Black (Pig) Meishan (Pig) | Dominant black | MC1R | E^D1 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.181883A>G | c.305T>C | p.(L102P) | Variant is called p.(L99P) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. | rs45434630 | 1998 | 9799269 | ||
| 1290 | OMIA:001199-9823 | pig | Large Black (Pig) Meishan (Pig) | Dominant black | MC1R | E^D1 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.181905C>T | c.283G>A | p.(V95M) | Variant is called p.(V92M) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. | rs45434629 | 1998 | 9799269 | ||
| 597 | OMIA:001199-9823 | pig | Bama Xiang Zhu, China (Pig) Pietrain (Pig) | Coat colour, black spotting on red or white background | MC1R | E^P, E^qy | insertion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.182126_182127insGG | c.67_68insCC | p.(R23Pfs*33) | Variant was published as nt67insCC (Kijas et al., 2001), g.462-463CC (Wu et al., 2017), c.67_68insCC (Jia et al. 2017) | rs1113295336 | 2001 | 28002929 28411032 11404341 | ||
| 1344 | OMIA:002217-9823 | pig | Fatness, growth, feed intake | MC4R | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 1 | g.160773437G>A | c.892G>A | p.(D298N) | ENSSSCT00000091644.1:c.892G>A ENSSSCP00000074588.1:p.Asp298Asn | rs81219178 | 2000 | 10656927 | Variant coordinates updated based on Johnsson and Jungnickel (2021) | |||
| 1378 | OMIA:001401-9823 | pig | Bama Xiang Zhu, China (Pig) | Waardenburg syndrome, type 2A | MITF | missense | Chemical mutagenesis (ENU) | Not currently ISAG evaluated | 13 | c.740T>C | p.(L247S) | 2017 | 29094203 | |||||||
| 849 | OMIA:001401-9823 | pig | Rongchang, China (Pig) | Waardenburg syndrome, type 2A | MITF | insertion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 13 | g.51377987_51377988insTTTAGTTTAAAAAA | a 14 bp insertion "in the non-regulatory region of the melanocyte-specific promoter of microphthalmia-associated transcription factor (MITF) gene generated a novel silencer" | 2016 | 27349893 | ||||||
| 1189 | OMIA:000319-9823 | pig | Ear size | MSRB3 | repeat variation | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 5 | "the 38.7-kb CNV . . . starts at 349,577 bp and ends at 388,246 bp of the corrected contig (MK028166) . . . , covering the last two exons 6 and 7 of the MSRB3 gene" (Chen et al., 2018) | 2018 | 30587124 | ||||||||
| 1019 | OMIA:002161-9823 | pig | Large White (Pig) | Leg weakness, MSTN-related | MSTN | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 15 | g.94623834C>A | c.820G>T | p.(E274*) | 2019 | 30699111 | |||||
| 441 | OMIA:000683-9823 | pig | Pietrain (Pig) | Muscular hypertrophy (double muscling) | MSTN | regulatory | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 15 | g.94629236T>C | Stinckens et al. (2008) describe polymorphism located at position 447 of the porcine MSTN promoter, EF490986 EF490990 g.447A>G | rs332188828 | 2008 | 18822098 | |||||
| 598 | OMIA:001200-9823 | pig | Tremor, high-frequency (Campus syndrome) | MYH7 | insertion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 7 | g.75668349_75668350insGGCGGG | c.4320_4321insCCCGCC | p.(A1440_A1441insPA) | 2012 | 23153285 | The genomic location on Sscrofa10.2 was determined by Stephanie Shields (27/05/2020) and updated to the genomic Sscrofa11.1 location by Imke Tammen | |||||
| 1316 | OMIA:002148-9823 | pig | Duroc (Pig) | Vestibular dysfunction | MYO7A | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 9 | g.11280403C>T | c.541C>T | p.(Q181*) | cDNA position is based on transcript NM_001099928.1 | 2021 | 33955556 | ||||
| 1370 | OMIA:002464-9823 | pig | Large White (Pig) | Cryopyrin-associated periodic syndrome | NLRP3 | missense | Genome editing (CRISPR/Cpf1) | Not currently ISAG evaluated | 2 | p.(R259W) | 2020 | 32958688 | ||||||||
| 1288 | OMIA:001128-9823 | pig | Duroc (Pig) | Pale soft exudative meat | PHKG1 | splicing | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 3 | g.16830320C>A | c.919-5C>A | ENSSSCT00000008491.4:c.919-5C>A Ma et al. 2014: "a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon" | rs330928088 | 2014 | 25340394 | ||||
| 1404 | OMIA:000807-9823 | pig | Polycystic kidney disease | PKD1 | PKD1^insG/+ | insertion, small (<=20) | Genome-editing (CRISPR-Cas9) | Not currently ISAG evaluated | 3 | c.152_153insG | 2022 | 34980882 | ||||||||
| 1406 | OMIA:000807-9823 | pig | Polycystic kidney disease | PKD1 | PKD1^Tins/+ | insertion, small (<=20) | Genome-editing (ZFN) | Not currently ISAG evaluated | 3 | c.642_643insT | 2015 | 25798056 | ||||||||
| 1405 | OMIA:000807-9823 | pig | Polycystic kidney disease | PKD1 | PKD1^TGCTins/+ | insertion, small (<=20) | Genome-editing (ZFN) | Not currently ISAG evaluated | 3 | c.642_643insTGCT | 2015 | 25798056 | ||||||||
| 1523 | OMIA:002525-9823 | pig | PKD2 overexpression | PKD2 | insertion, gross (>20) | Genome-editing (CRISPR-Cas9) | Not currently ISAG evaluated | insertion of transgene vector pCAG-muhPKD2 (c.1532A > T/p.511D > V)-3 × FLAG-floxP-neo-pH11 into the pH11 safe harbor site | 2022 | 36452154 | ||||||||||
| 1054 | OMIA:002183-9823 | pig | Landrace (Pig) | Embryonic lethality | PNKP | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.54880241T>C | p.(Q96R) | Derks et al. (2019): "deleterious missense mutation in the PNKP gene (6:g.54880241G>T), predicted to be strongly deleterious by SIFT (0.02) and PROVEAN (-2.9). The missense mutation causes a glutamine to arginine amino acid substitution (ENSSSCP00000003467:p.Gln96Arg)" | 2019 | 30875370 | |||||
| 1052 | OMIA:002181-9823 | pig | Landrace (Pig) | Embryonic lethality | POLR1B | splicing | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 3 | g.43952776T>G | Derks et al. (2019): "Skipping of exon 14 introduces a glutamic acid and a premature stop codon in the second codon of the terminal exon, lacking the final 370 amino acids located in the conserved subunit 2, hybrid-binding domain (binding to the DNA strand)" | 2019 | 30875370 | ||||||
| 173 | OMIA:001579-9823 | pig | Taihu - Erhualian, China (Pig) | Large floppy ears | PPARD | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 7 | g.31281804G>A | c.95G>A | p.(G32E) | rs80909573 | 2011 | 21573137 | The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcripts: XM_005665910.3, XM_013977808.2 by Stephanie Shields (27/05/2020) | |||
| 175 | OMIA:001085-9823 | pig | Meat quality (Rendement Napole) | PRKAG3 | RN- | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 15 | g.120863533C>T | c.749G>A | p.(R250Q) | The paper by Milan et al. (2000) reported this variant as c.599G>A and p.R200Q | rs1109104772 | 2000 | 10818001 | The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: ENSSSCT00000017641.4 by Stephanie Shields (27/05/2020) | ||
| 176 | OMIA:001085-9823 | pig | Meat quality (Rendement Napole) | PRKAG3 | RN- | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 15 | g.120863537C>T | c.745G>A | p.(I249V) | rs1108399077 | 2001 | 11729159 | he genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: ENSSSCT00000017641.4 by Stephanie Shields (27/05/2020) | |||
| 174 | OMIA:000621-9823 | pig | Malignant hyperthermia | RYR1 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.47357966T>C | c.1843C>T | p.(R615C) | NM_001001534.1: c.1843C>T; p.(R615C) Interestingly, the reference allele in the Sscrofa11.1 assembly is T rather than C, meaning that the Duroc animal that is the basis of this reference genome assembly has the causal variant for malignant hyperthermia! | rs344435545 | 1991 | 1862346 | Effect was confirmed with Ensembl VEP in the following transcript: NM_001001534.1 by Stephanie Shields (27/05/2020) | |||
| 1367 | OMIA:002453-9823 | pig | Waardenburg syndrome | SOX10 | duplication | Genome-editing (CRISPR-Cas9) | Not currently ISAG evaluated | 5 | c.321dupC | p.(K108Qfs*45) | 2016 | 26442986 | ||||||||
| 1366 | OMIA:002453-9823 | pig | Bama Xiang Zhu, China (Pig) | Waardenburg syndrome | SOX10 | missense | Chemical mutagenesis (ENU) | Not currently ISAG evaluated | 5 | c.325A>T | p.(R109W) | 2017 | 28639938 | |||||||
| 392 | OMIA:002435-9823 | pig | Sperm, short tail | SPEF2 | splicing | Naturally occurring variant | Not currently ISAG evaluated | 16 | an inserted retrotransposon within an intron | 2006 | 16549801 | |||||||||
| 1149 | OMIA:002232-9823 | pig | Large White (Pig) | Myopathy, congenital, SPTBN4-related | SPTBN4 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 6 | g.48801281_48801296del | p.(R1902fs) | Derks et al. (2019): ENSSSCP00000031537:p.Arg1902fs | 2019 | 31850074 | |||||
| 1668 | OMIA:002829-9823 | pig | Porcine circovirus type 2, association with reduced viral load | SYNGR2 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa 11.1 | 12 | g.3797515A>G | c.186T>C | p.(R63C) | XM_021066554.1; XP_020922213.1 | rs3473454700 | 2018 | 30379811 | ||||
| 1051 | OMIA:002180-9823 | pig | Duroc (Pig) | Embryonic lethality | TADA2A | splicing | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 12 | g.38922102G>A | splice-donor mutation causing retention of intron 13 or exon skipping of exon 13 (Derks et al., 2019) | 2019 | 30875370 | ||||||
| 912 | OMIA:001673-9823 | pig | Large White, Finland (Pig) | Spermatogenic arrest | TEX14 | splicing | Naturally occurring variant | Not currently ISAG evaluated | 12 | "a 51 bp insertion within exon 27, which caused differential splicing of the exon and created a premature translation stop codon" | 2011 | 22136159 | ||||||||
| 1519 | OMIA:001472-9823 | pig | Yucatan Miniature, United States of America (Pig) | Neuronal ceroid lipfuscinosis, 2 (CLN2) | TPP1 | nonsense (stop-gain) | Transgenesis via viral vectors | Not currently ISAG evaluated | p.(R208X) | 2022 | 36100791 | |||||||||
| 508 | OMIA:001249-9823 | pig | Dahe, China (Pig) Tibetan, China (Pig) Wujin - Kele, China (Pig) Wujin - Liangshan, China (Pig) | Brown | TYRP1 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 1 | g.209726927_209726932del | c.1484_1489del | p.(M495_G496del) | 2011 | 20978532 | |||||
| 931 | OMIA:001436-9823 | pig | Non-shivering thermiogenesis, absence of | UCP1 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 8 | "exons 3 to 5 were eliminated by a deletion in the pig sequence" | 2006 | 16933999 | |||||||||
| 1053 | OMIA:002182-9823 | pig | Landrace (Pig) | Embryonic lethality | URB1 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 13 | g.195977038del | p.(V1961fs) | Derks et al. (2019): "[a] frameshift mutation in exon 38 of the URB1 gene (13:g.195977038delC) caused by a 1-bp deletion . . . The frameshift (ENSSSCP00000036505:p.Val1961fs) introduces 26 novel amino acids and a premature stop codon, producing a truncated protein of 1,986 amino acids, lacking the final 261 amino acids compared to the wild-type protein (2,247 AA)." | 2019 | 30875370 | |||||
| 969 | OMIA:001058-9823 | pig | Mixed Breed (Dog) | Von Willebrand disease III | VWF | duplication | Naturally occurring variant | Not currently ISAG evaluated | 5 | p.(V814Lfs*3) | "a tandem duplication of exons 17 and 18, causing a frameshift and a premature termination codon (p.Val814LeufsTer3) . . . This duplication putatively originates from porcine SINE elements located within VWF introns 16 and 18 with high identity. | 2018 | 29208651 | |||||||
| 1033 | OMIA:001579-9823 | pig | Large White (Pig) Min, China (Pig) | Ear size | WIF1 | missense | Naturally occurring variant | Not currently ISAG evaluated | Sscrofa11.1 | 5 | g.29463165C>G | c.1167C>G | p.(F236L) | rs338733115 | 2019 | 30815903 | ||||
| 1376 | OMIA:002468-9823 | pig | Bama Xiang Zhu, China (Pig) | ZBED6 knock-out | ZBED6 | deletion, small (<=20) | Genome-editing (CRISPR-Cas9) | Not currently ISAG evaluated | c.1320del | c.1320del causes a frameshift after codon 134 and a premature stop occurs at codon 224 (Wang et al., 2021) | 2021 | 34710100 |
* Variant pathogenicity for single gene diseases as evaluated by an expert panel of the International Society of Animal Genetics (ISAG) Animal Genetic Testing Standardization Standing Committee
| Overall Statistics | |
|---|---|
| Total number of variants | 73 |
| Variants with genomic location | 48 (65.8% ) |
| Variants in a variant database, i.e. with rs ID | 19 (26.0%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 2 | 2.7% |
| deletion, gross (>20) | 10 | 13.7% |
| deletion, small (<=20) | 6 | 8.2% |
| delins, gross (>20) | 1 | 1.4% |
| delins, small (<=20) | 1 | 1.4% |
| duplication | 3 | 4.1% |
| insertion, gross (>20) | 3 | 4.1% |
| insertion, small (<=20) | 6 | 8.2% |
| missense | 24 | 32.9% |
| nonsense (stop-gain) | 5 | 6.8% |
| not known | 1 | 1.4% |
| regulatory | 1 | 1.4% |
| repeat variation | 1 | 1.4% |
| splicing | 9 | 12.3% |
| Variant Effect | Count | Percent |
|---|---|---|
| unknown | 73 | 100.0% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1991 | 1 | 1.4% |
| 1992 | 0 | 0.0% |
| 1993 | 0 | 0.0% |
| 1994 | 0 | 0.0% |
| 1995 | 0 | 0.0% |
| 1996 | 1 | 1.4% |
| 1997 | 0 | 0.0% |
| 1998 | 7 | 9.6% |
| 1999 | 0 | 0.0% |
| 2000 | 4 | 5.5% |
| 2001 | 2 | 2.7% |
| 2002 | 1 | 1.4% |
| 2003 | 2 | 2.7% |
| 2004 | 1 | 1.4% |
| 2005 | 0 | 0.0% |
| 2006 | 2 | 2.7% |
| 2007 | 0 | 0.0% |
| 2008 | 1 | 1.4% |
| 2009 | 0 | 0.0% |
| 2010 | 0 | 0.0% |
| 2011 | 5 | 6.8% |
| 2012 | 3 | 4.1% |
| 2013 | 1 | 1.4% |
| 2014 | 1 | 1.4% |
| 2015 | 5 | 6.8% |
| 2016 | 4 | 5.5% |
| 2017 | 2 | 2.7% |
| 2018 | 5 | 6.8% |
| 2019 | 11 | 15.1% |
| 2020 | 4 | 5.5% |
| 2021 | 5 | 6.8% |
| 2022 | 5 | 6.8% |